Microarrays are commonly fabricated by locating biomolecules onto flat substrates. Known technologies of microarray fabrication can be divided into two methods:    1) The position of the biomolecule is specified prior to its transfer on the substrate (“Ordered biomolecule deposition”); and    2) The position of the biomolecule is randomly allocated on the substrate (“Random biomolecule deposition”).
Ordered biomolecule deposition is by far the most usual way for microarray production. A detailed experimental description is given in: Schena, M., “DNA Microarrays”, Oxford University Press, 2001. A technology review is also given in: Vivian G., at al. “Making and reading microarrays”, Nature Genetics 21, 15-19, 1999. In known microarray production methods, robots carry out the transfer of analyte-targeting biomolecules to substrates and ordered arrays are created. Usually biomolecules are dissolved in a buffer. Typical transfer volumes are between 0.1 nl and 1 ml. Examples of biomolecules are DNA, oligonucleotides and proteins.
Different technologies are available to spot the biomolecule solution onto the substrate. Spotting technologies can be divided in two groups:                1) Technologies that have no physical contact between the printer and the surface; and        2) Technologies that make use of physical contact between a printing tip and the substrate.        
Technologies that belong to the first group are based on bubble-jet technologies in which a small droplet is produced and accelerated by means of piezoelectric induced or thermal induced pressure, or with the production of a droplet with a motor driven micro syringe (Okamoto T., et al. “Microarray fabrication with covalent attachment of DNA using Bubble Jet technology”, Nature Biotechnology, 18, 438-441, 2000).
Technologies that belong to the second group use a printing tip that can hold a small volume of a sample solution and transfer a part of this solution to the substrate by making physical contact. The transferred volume depends on the print tip geometry, nature of the solvent and the hydrophobicity of the substrate.
In all of the abovementioned technologies, print heads or pins can be combined into groups (usually 8 to 64) to print multiple samples in parallel. The distance of spots printed in parallel is fixed due to the physical size of the printer heads or pins. This limits the minimal spot distance to 2 to 5 mm in a parallel printing step. To archive high spot density, multiple prints must be carried out with a small offset in the x and/or y direction.
In all of the above known methods, the number of spots printed is linear to the product of print heads and printing steps, thus limiting the production of high quantities of arrays.
The production time increases linearly with the number of chips produced and with the number of particular bio-recognition elements printed. The array density is limited due to the accuracy of the printing instrument. The disadvantage of robot-based techniques is the long time needed to produce a large number of arrays with high spot density.
Another microarray production technology is based on the synthesis of polymers directly onto the microarray substrate and is described in International PCT Patent Publication Number WO 9210092 and U.S. Pat. Nos. 5,405,783 and 5,770,722. These disclosed techniques are limited to oligonucleotides and utilize photolithography. The disclosed techniques are only economic if a very high number (thousands) of different oligonucleotide sequences are needed.
In random biomolecule deposition, biomolecule spots are created randomly onto a substrate. Common techniques use mixtures of microbeads or microbeads made from subpopulations. To determine which subpopulation a microbead belongs to, all of the microbeads must be encoded. Technologies to encode microbeads are based on their labeling with fluorophores of different color, labeling with micro microbeads carrying different colors (WO2004066210 HYBRID RANDOM BEAD/CHIP BASED MICROARRAY), by metal tags (Lockhart, D. J., at al. “Multiplex Metallica”, Nature Biotechnology, 19, 1122-1123, 2001), by radio frequency tags, by fluorescence energy transfer tags (Tong, A. K., at al. “Combinatorial fluorescence energy transfer tags for multiplex biological assays”, Nature Biotechnology, 19, 756-759, 2001), by oligonucleotide tags or with quantum-dots (Han, M., at al. “Quantum-dot-tagged microbeads for multiplexed optical coding of biomolecules”, Nature Biotechnology 19, 631-635, 2001). Encoding by optical signatures (e.g. fluorescence) is further described in International PCT Patent Publication Numbers WO 0016101, WO 0061281, and WO 9853093. Methods that make use of fiber optic bundles with dyes attached to their distal ends instead of flat substrates are described in U.S. Pat. No. 5,244,636 and U.S. Pat. No. 5,250,264. The advantage of using optical fibers is to avoid the problem of interference of light which may arise from the use of different dyes.
Large numbers of polystyrene beads (˜3.2 μm) can be assembled into a high density bead array chip in an etched silicon device by a method known as light-controlled electrokinetic assembly of microbeads near surfaces (LEAPS) (Li et al. Tissue Antigens 63: 518-528). In this method, the back side of a silicon wafer is placed in contact with a metal electrode. A counter electrode is then brought into contact with a suspended bead solution that is dispensed onto the wafer surface. Using an alternating current, beads can be moved to designated areas of low-impedance on the chip. An array of about 4000 beads has been successfully arrayed in a 300 μm×300 μm area, and applied in Single Nucleotide Polymorphism (SNP) analysis of the human leukocyte antigen gene complex. Although the analysis times are not reported, the ability to assemble thousands of individually addressable beads makes this bead array chip an attractive platform for high-throughput SNP genotyping.
In known methods, the information of individual spots or beads is deciphered after all of the beads have been randomly placed on the substrate, typically at the same time the array is used for analysis. The microbeads are decoded and the decode data is combined with data obtained from reading changes of microbead properties caused by the analyte. Automated information processing for decoding of encoded microbeads is described in International PCT Patent Publication Number WO 0047996.
A disadvantage of decoding procedures associated with such methods as those disclosed in WO 0047996 is that the decoding step can be complex and time consuming. In WO 0047996, the decoding step requires that a first plurality of decoding binding ligands are added to a random array of microbeads comprising immobilized binding ligands and a first data image is created. A fiducial is used to generate a first registered data image. A second plurality of decoding binding ligands are added to the random array of microbeads and a second data image is created. The fiducial is used to generate a second registered data image. A computer system is then used to compare the first and the second registered data images to identify the location of at least two bioactive agents. However, the use of decoding binding ligands taught in WO 0047996 has significant disadvantages. In particular, a long time is needed to read the encoded code of all microbeads, as discussed in: Nolan J. P. et al. “Suspension array technology: evolution of the flat-array paradigm”, Trends in Biotechnology, 20, 9-12, 2002.
Furthermore the creation of an encoding system is difficult and requires multiple processing steps. Read out instruments are required to decode encoded microbeads. For example, microbead code created by different fluorophores require multiple wavelength measurements, thereby requiring multiple light sources and filters. These instruments are sophisticated and expensive. All of the above factors make manufacturing the microarrays more complex, time consuming and thereby more expensive to implement.
There is a need to provide a process for making micro-arrays that overcomes, or at least ameliorates, one or more of the disadvantages described above.
There is a need to provide a system for identifying the presence of a target analyte that overcomes, or at least ameliorates, one or more of the disadvantages described above.
There is a need to provide a process for making microarrays that avoids the need to decode the microarrays after manufacture.